MolNFT v1 · #116813 · protein
The structure of PKMT1 from rickettsia prowazekii in complex with adomet
5DPD · Protein lysine methyltransferase 1: “The structure of PKMT1 from rickettsia prowazekii in complex with adomet”. X-ray diffraction, 1 ligand (SAM), 16 pockets (best druggability 0.67). MolNFT v1 #116813 on GenesisL1: 3D structure…
- PDB
- 5DPD
- Type
- protein
- Length
- 1,022 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein lysine methyltransferase 1
- UniProt
- O05979
- Ligands
- SAM
- Pockets
- 16 · best druggability 0.67
Structure
x-ray diffraction · 1 distinct chain · 42% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Protein lysine methyltransferase 1 | protein | 511 | 42% helix, 15% strand | O05979 |
Ligands and binding sites
- SAM · S-adenosylmethionine · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 338 | 0.67 | 0.81 | 44 | empty |
| 2 | 558 | 0.64 | 0.75 | 53 | SAM |
| 3 | 570 | 0.63 | 0.75 | 50 | SAM |
| 4 | 144 | 0.59 | 0.83 | 18 | empty |
| 5 | 255 | 0.59 | 0.79 | 28 | empty |
Interfaces
1 interface between chains.
- A–B · 1595 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 5DPD · The structure of PKMT1 from Rickettsia prowazekii in complex with AdoMet · the same entry in another collection · chain A against A, TM-score 1.00
- O05979 · AlphaFold monomer V2.0 prediction for uncharacterized protein RP789 (O05979) · a predicted model of the same protein · chain A against A, TM-score 0.97
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt O05979
- Elsewhere: RCSB PDB 5DPD · PDBe 5DPD · UniProt O05979
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